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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.25.1

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-07-10, 09:23 CEST based on data in: /scratch/mcarazo/ongoing/GB/sRNAseq_may25/trim_galore_out/fastqc_results


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        General Statistics

        Showing 0/172 rows and 4/6 columns.
        Sample NameDupsGCAvg lenMedian lenFailedSeqs
        CV_GBM_C009_R1_val_1
        97.8%
        58.0%
        44bp
        37bp
        45%
        30.5M
        CV_GBM_C009_R2_val_2
        97.2%
        59.0%
        45bp
        37bp
        45%
        30.5M
        CV_GBM_C010_R1_val_1
        97.0%
        58.0%
        42bp
        37bp
        45%
        20.0M
        CV_GBM_C010_R2_val_2
        96.5%
        58.0%
        43bp
        37bp
        45%
        20.0M
        CV_GBM_C011_R1_val_1
        97.7%
        58.0%
        44bp
        37bp
        45%
        27.7M
        CV_GBM_C011_R2_val_2
        97.3%
        59.0%
        44bp
        37bp
        45%
        27.7M
        CV_GBM_C016_R1_val_1
        97.8%
        58.0%
        47bp
        42bp
        45%
        18.6M
        CV_GBM_C016_R2_val_2
        97.3%
        59.0%
        48bp
        42bp
        45%
        18.6M
        CV_GBM_C018_R1_val_1
        97.7%
        58.0%
        47bp
        37bp
        45%
        24.1M
        CV_GBM_C018_R2_val_2
        97.2%
        58.0%
        47bp
        37bp
        45%
        24.1M
        CV_GBM_C019_R1_val_1
        97.9%
        58.0%
        53bp
        42bp
        45%
        20.9M
        CV_GBM_C019_R2_val_2
        97.2%
        58.0%
        53bp
        47bp
        45%
        20.9M
        CV_GBM_C020_R1_val_1
        97.8%
        57.0%
        47bp
        37bp
        45%
        28.8M
        CV_GBM_C020_R2_val_2
        97.2%
        58.0%
        47bp
        37bp
        45%
        28.8M
        CV_GBM_C028_R1_val_1
        93.4%
        59.0%
        30bp
        22bp
        45%
        1.6M
        CV_GBM_C028_R2_val_2
        92.7%
        60.0%
        31bp
        22bp
        45%
        1.6M
        CV_GBM_C029_R1_val_1
        96.3%
        58.0%
        39bp
        32bp
        45%
        4.8M
        CV_GBM_C029_R2_val_2
        95.6%
        59.0%
        39bp
        32bp
        45%
        4.8M
        CV_GBM_C030_R1_val_1
        97.1%
        58.0%
        36bp
        32bp
        45%
        9.7M
        CV_GBM_C030_R2_val_2
        96.6%
        59.0%
        36bp
        32bp
        45%
        9.7M
        CV_GBM_C031_R1_val_1
        96.7%
        59.0%
        41bp
        32bp
        45%
        5.6M
        CV_GBM_C031_R2_val_2
        96.1%
        59.0%
        41bp
        32bp
        45%
        5.6M
        CV_GBM_C033_R1_val_1
        97.9%
        57.0%
        42bp
        32bp
        45%
        14.6M
        CV_GBM_C033_R2_val_2
        97.4%
        57.0%
        42bp
        32bp
        45%
        14.6M
        CV_GBM_C035_R1_val_1
        98.0%
        57.0%
        47bp
        42bp
        45%
        22.5M
        CV_GBM_C035_R2_val_2
        97.3%
        58.0%
        47bp
        42bp
        45%
        22.5M
        CV_GBM_C036_R1_val_1
        98.0%
        56.0%
        50bp
        47bp
        45%
        27.1M
        CV_GBM_C036_R2_val_2
        97.5%
        57.0%
        51bp
        47bp
        45%
        27.1M
        CV_GBM_C039_R1_val_1
        97.9%
        57.0%
        39bp
        32bp
        45%
        11.1M
        CV_GBM_C039_R2_val_2
        97.4%
        57.0%
        39bp
        32bp
        45%
        11.1M
        CV_GBM_C049_R1_val_1
        98.5%
        57.0%
        44bp
        32bp
        45%
        19.4M
        CV_GBM_C049_R2_val_2
        97.9%
        58.0%
        44bp
        32bp
        45%
        19.4M
        CV_GBM_C050_R1_val_1
        97.6%
        58.0%
        43bp
        32bp
        45%
        25.3M
        CV_GBM_C050_R2_val_2
        97.0%
        58.0%
        43bp
        32bp
        45%
        25.3M
        DC_1023_R1_val_1
        98.5%
        58.0%
        49bp
        42bp
        45%
        19.7M
        DC_1023_R2_val_2
        97.9%
        58.0%
        49bp
        42bp
        45%
        19.7M
        DC_1027_R1_val_1
        98.7%
        59.0%
        48bp
        42bp
        45%
        22.8M
        DC_1027_R2_val_2
        98.0%
        59.0%
        48bp
        42bp
        45%
        22.8M
        DC_1030_R1_val_1
        98.2%
        58.0%
        49bp
        42bp
        45%
        24.6M
        DC_1030_R2_val_2
        97.4%
        59.0%
        49bp
        42bp
        45%
        24.6M
        DC_1032_R1_val_1
        98.4%
        58.0%
        56bp
        47bp
        45%
        23.4M
        DC_1032_R2_val_2
        97.8%
        58.0%
        56bp
        47bp
        45%
        23.4M
        DC_1037_R1_val_1
        98.2%
        58.0%
        53bp
        47bp
        45%
        16.6M
        DC_1037_R2_val_2
        97.6%
        58.0%
        53bp
        47bp
        45%
        16.6M
        DC_2011_R1_val_1
        98.3%
        59.0%
        47bp
        42bp
        45%
        21.2M
        DC_2011_R2_val_2
        97.7%
        60.0%
        47bp
        42bp
        45%
        21.2M
        DC_2012_R1_val_1
        98.1%
        59.0%
        60bp
        52bp
        45%
        28.8M
        DC_2012_R2_val_2
        97.4%
        59.0%
        60bp
        52bp
        45%
        28.8M
        DC_2014_R1_val_1
        98.4%
        58.0%
        41bp
        42bp
        45%
        25.2M
        DC_2014_R2_val_2
        98.0%
        58.0%
        42bp
        42bp
        45%
        25.2M
        DC_2017_R1_val_1
        98.1%
        58.0%
        54bp
        47bp
        45%
        26.1M
        DC_2017_R2_val_2
        97.4%
        58.0%
        54bp
        47bp
        45%
        26.1M
        DC_2019_R1_val_1
        98.2%
        58.0%
        50bp
        47bp
        45%
        31.0M
        DC_2019_R2_val_2
        97.7%
        58.0%
        50bp
        47bp
        45%
        31.0M
        DC_3007_R1_val_1
        98.4%
        58.0%
        48bp
        42bp
        45%
        22.5M
        DC_3007_R2_val_2
        97.8%
        58.0%
        48bp
        42bp
        45%
        22.5M
        DC_3024_R1_val_1
        98.6%
        57.0%
        54bp
        47bp
        45%
        27.0M
        DC_3024_R2_val_2
        98.1%
        57.0%
        54bp
        47bp
        45%
        27.0M
        DC_3028_R1_val_1
        98.5%
        58.0%
        48bp
        47bp
        45%
        19.8M
        DC_3028_R2_val_2
        98.0%
        58.0%
        48bp
        47bp
        45%
        19.8M
        DC_3030_R1_val_1
        98.4%
        58.0%
        47bp
        42bp
        45%
        21.4M
        DC_3030_R2_val_2
        98.0%
        58.0%
        48bp
        42bp
        45%
        21.4M
        DC_3031_R1_val_1
        98.6%
        58.0%
        51bp
        47bp
        45%
        27.0M
        DC_3031_R2_val_2
        98.2%
        58.0%
        51bp
        47bp
        45%
        27.0M
        DC_3042_R1_val_1
        98.2%
        58.0%
        62bp
        52bp
        45%
        29.8M
        DC_3042_R2_val_2
        97.6%
        58.0%
        62bp
        52bp
        45%
        29.8M
        DC_3047_R1_val_1
        98.1%
        58.0%
        60bp
        52bp
        45%
        27.1M
        DC_3047_R2_val_2
        97.4%
        58.0%
        60bp
        52bp
        45%
        27.1M
        DC_3049_R1_val_1
        97.8%
        58.0%
        59bp
        52bp
        45%
        28.2M
        DC_3049_R2_val_2
        97.1%
        58.0%
        60bp
        52bp
        45%
        28.2M
        DC_3051_R1_val_1
        97.8%
        58.0%
        63bp
        57bp
        45%
        25.7M
        DC_3051_R2_val_2
        97.3%
        58.0%
        63bp
        57bp
        45%
        25.7M
        DC_3059_R1_val_1
        98.2%
        58.0%
        62bp
        57bp
        45%
        31.2M
        DC_3059_R2_val_2
        97.6%
        58.0%
        62bp
        57bp
        45%
        31.2M
        DC_3060_R1_val_1
        97.8%
        58.0%
        54bp
        47bp
        45%
        26.9M
        DC_3060_R2_val_2
        97.3%
        58.0%
        55bp
        47bp
        45%
        26.9M
        DC_3079_R1_val_1
        98.3%
        58.0%
        53bp
        47bp
        45%
        27.1M
        DC_3079_R2_val_2
        97.7%
        58.0%
        54bp
        47bp
        45%
        27.1M
        DC_3083_R1_val_1
        98.4%
        58.0%
        48bp
        42bp
        45%
        26.2M
        DC_3083_R2_val_2
        97.8%
        59.0%
        48bp
        42bp
        45%
        26.2M
        DC_3099_R1_val_1
        98.2%
        57.0%
        64bp
        57bp
        45%
        20.5M
        DC_3099_R2_val_2
        97.7%
        58.0%
        65bp
        57bp
        45%
        20.5M
        DC_3112_R1_val_1
        98.2%
        58.0%
        50bp
        47bp
        45%
        17.7M
        DC_3112_R2_val_2
        97.6%
        58.0%
        51bp
        47bp
        45%
        17.7M
        DC_3117_R1_val_1
        98.2%
        58.0%
        44bp
        42bp
        45%
        26.1M
        DC_3117_R2_val_2
        97.8%
        59.0%
        44bp
        42bp
        45%
        26.1M
        GB22_32_R1_val_1
        98.2%
        59.0%
        54bp
        47bp
        45%
        38.2M
        GB22_32_R2_val_2
        97.7%
        59.0%
        54bp
        47bp
        45%
        38.2M
        GB22_33_R1_val_1
        98.1%
        60.0%
        42bp
        32bp
        45%
        34.8M
        GB22_33_R2_val_2
        97.4%
        60.0%
        42bp
        37bp
        45%
        34.8M
        GB23_01_R1_val_1
        98.2%
        59.0%
        52bp
        47bp
        45%
        30.4M
        GB23_01_R2_val_2
        97.8%
        59.0%
        53bp
        47bp
        45%
        30.4M
        GB23_03_R1_val_1
        98.3%
        58.0%
        64bp
        57bp
        45%
        31.9M
        GB23_03_R2_val_2
        97.8%
        58.0%
        64bp
        57bp
        45%
        31.9M
        GB23_05_R1_val_1
        98.1%
        58.0%
        65bp
        57bp
        45%
        20.3M
        GB23_05_R2_val_2
        97.4%
        58.0%
        66bp
        57bp
        45%
        20.3M
        GB23_06_R1_val_1
        98.4%
        58.0%
        62bp
        57bp
        45%
        18.0M
        GB23_06_R2_val_2
        97.9%
        58.0%
        62bp
        57bp
        45%
        18.0M
        GB23_08_R1_val_1
        98.4%
        58.0%
        63bp
        57bp
        45%
        28.5M
        GB23_08_R2_val_2
        97.9%
        58.0%
        63bp
        57bp
        45%
        28.5M
        GB23_11_R1_val_1
        98.2%
        58.0%
        59bp
        57bp
        45%
        22.1M
        GB23_11_R2_val_2
        97.7%
        58.0%
        60bp
        57bp
        45%
        22.1M
        GB23_12_R1_val_1
        97.9%
        57.0%
        48bp
        42bp
        45%
        14.3M
        GB23_12_R2_val_2
        97.3%
        58.0%
        48bp
        42bp
        45%
        14.3M
        GB23_14_R1_val_1
        98.4%
        58.0%
        50bp
        47bp
        45%
        19.3M
        GB23_14_R2_val_2
        97.8%
        58.0%
        50bp
        47bp
        45%
        19.3M
        GB23_16_R1_val_1
        98.1%
        58.0%
        55bp
        47bp
        45%
        11.9M
        GB23_16_R2_val_2
        97.6%
        58.0%
        55bp
        47bp
        45%
        11.9M
        GB23_17_R1_val_1
        98.3%
        58.0%
        58bp
        52bp
        45%
        23.5M
        GB23_17_R2_val_2
        97.8%
        58.0%
        58bp
        52bp
        45%
        23.5M
        GB23_18_R1_val_1
        98.2%
        58.0%
        55bp
        47bp
        45%
        17.5M
        GB23_18_R2_val_2
        97.7%
        58.0%
        55bp
        47bp
        45%
        17.5M
        GB23_20_R1_val_1
        98.4%
        57.0%
        53bp
        47bp
        45%
        24.9M
        GB23_20_R2_val_2
        97.9%
        57.0%
        53bp
        47bp
        45%
        24.9M
        GB23_22_R1_val_1
        98.3%
        58.0%
        54bp
        47bp
        45%
        16.7M
        GB23_22_R2_val_2
        97.7%
        58.0%
        54bp
        47bp
        45%
        16.7M
        GB23_26_R1_val_1
        98.2%
        58.0%
        58bp
        52bp
        45%
        22.0M
        GB23_26_R2_val_2
        97.6%
        58.0%
        58bp
        52bp
        45%
        22.0M
        GB23_27_R1_val_1
        98.3%
        57.0%
        60bp
        57bp
        45%
        28.4M
        GB23_27_R2_val_2
        97.7%
        58.0%
        60bp
        57bp
        45%
        28.4M
        GB23_28_R1_val_1
        98.2%
        58.0%
        57bp
        52bp
        45%
        21.6M
        GB23_28_R2_val_2
        97.6%
        58.0%
        57bp
        52bp
        45%
        21.6M
        GB23_32_R1_val_1
        98.5%
        58.0%
        59bp
        57bp
        45%
        19.8M
        GB23_32_R2_val_2
        97.8%
        58.0%
        59bp
        57bp
        45%
        19.8M
        GB23_33_R1_val_1
        98.7%
        58.0%
        59bp
        57bp
        45%
        23.5M
        GB23_33_R2_val_2
        98.1%
        58.0%
        59bp
        57bp
        45%
        23.5M
        GB23_36_R1_val_1
        98.3%
        58.0%
        57bp
        52bp
        45%
        18.7M
        GB23_36_R2_val_2
        97.7%
        58.0%
        57bp
        52bp
        45%
        18.7M
        GB23_40_R1_val_1
        98.4%
        58.0%
        55bp
        47bp
        45%
        28.2M
        GB23_40_R2_val_2
        97.8%
        58.0%
        55bp
        52bp
        45%
        28.2M
        GB23_42_R1_val_1
        97.8%
        58.0%
        61bp
        57bp
        45%
        22.2M
        GB23_42_R2_val_2
        97.2%
        58.0%
        61bp
        57bp
        45%
        22.2M
        GB23_47_R1_val_1
        98.0%
        57.0%
        59bp
        57bp
        45%
        23.3M
        GB23_47_R2_val_2
        97.4%
        58.0%
        59bp
        57bp
        45%
        23.3M
        GB23_49_R1_val_1
        98.7%
        58.0%
        57bp
        52bp
        45%
        28.4M
        GB23_49_R2_val_2
        98.1%
        58.0%
        57bp
        52bp
        45%
        28.4M
        GB23_50_R1_val_1
        98.4%
        58.0%
        59bp
        57bp
        45%
        27.4M
        GB23_50_R2_val_2
        97.9%
        58.0%
        59bp
        57bp
        45%
        27.4M
        GB23_52_R1_val_1
        98.2%
        58.0%
        63bp
        57bp
        45%
        26.7M
        GB23_52_R2_val_2
        97.6%
        58.0%
        63bp
        57bp
        45%
        26.7M
        GB23_56_R1_val_1
        98.6%
        59.0%
        55bp
        47bp
        45%
        17.3M
        GB23_56_R2_val_2
        98.1%
        59.0%
        55bp
        47bp
        45%
        17.3M
        GB23_57_R1_val_1
        98.6%
        58.0%
        52bp
        47bp
        45%
        27.4M
        GB23_57_R2_val_2
        98.1%
        58.0%
        53bp
        47bp
        45%
        27.4M
        GB23_58_R1_val_1
        98.6%
        57.0%
        54bp
        47bp
        45%
        24.7M
        GB23_58_R2_val_2
        98.2%
        58.0%
        54bp
        47bp
        45%
        24.7M
        GB23_59_R1_val_1
        98.6%
        57.0%
        45bp
        42bp
        45%
        18.6M
        GB23_59_R2_val_2
        98.3%
        57.0%
        45bp
        42bp
        45%
        18.6M
        GB24_01_R1_val_1
        98.4%
        58.0%
        56bp
        52bp
        45%
        11.2M
        GB24_01_R2_val_2
        97.8%
        58.0%
        56bp
        52bp
        45%
        11.2M
        GB24_02_R1_val_1
        98.2%
        58.0%
        52bp
        47bp
        45%
        33.0M
        GB24_02_R2_val_2
        97.5%
        58.0%
        53bp
        47bp
        45%
        33.0M
        GB24_04_R1_val_1
        98.3%
        58.0%
        58bp
        52bp
        45%
        18.3M
        GB24_04_R2_val_2
        97.7%
        58.0%
        58bp
        52bp
        45%
        18.3M
        GB24_05_R1_val_1
        98.3%
        58.0%
        56bp
        47bp
        45%
        24.7M
        GB24_05_R2_val_2
        97.6%
        59.0%
        56bp
        47bp
        45%
        24.7M
        GB24_14_R1_val_1
        97.5%
        58.0%
        60bp
        57bp
        45%
        17.2M
        GB24_14_R2_val_2
        96.6%
        58.0%
        61bp
        57bp
        45%
        17.2M
        GB24_20_R1_val_1
        98.4%
        58.0%
        59bp
        52bp
        45%
        33.2M
        GB24_20_R2_val_2
        97.9%
        58.0%
        59bp
        52bp
        45%
        33.2M
        GB24_21_R1_val_1
        98.2%
        58.0%
        57bp
        47bp
        45%
        24.7M
        GB24_21_R2_val_2
        97.6%
        58.0%
        57bp
        52bp
        45%
        24.7M
        GB24_29_R1_val_1
        98.0%
        58.0%
        62bp
        57bp
        45%
        25.4M
        GB24_29_R2_val_2
        97.4%
        58.0%
        62bp
        57bp
        45%
        25.4M
        GB24_32_R1_val_1
        97.8%
        58.0%
        61bp
        52bp
        45%
        30.4M
        GB24_32_R2_val_2
        97.1%
        58.0%
        61bp
        52bp
        45%
        30.4M
        GB24_33_R1_val_1
        97.0%
        58.0%
        57bp
        52bp
        45%
        12.5M
        GB24_33_R2_val_2
        96.4%
        58.0%
        58bp
        52bp
        45%
        12.5M
        GB24_37_R1_val_1
        97.9%
        58.0%
        54bp
        47bp
        45%
        27.9M
        GB24_37_R2_val_2
        97.4%
        59.0%
        54bp
        47bp
        45%
        27.9M
        GB24_39_R1_val_1
        98.0%
        58.0%
        73bp
        62bp
        45%
        11.8M
        GB24_39_R2_val_2
        97.3%
        58.0%
        73bp
        62bp
        45%
        11.8M

        FastQC

        Version: 0.12.1

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 0/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        ACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTG
        86
        109815624
        2.8063%
        AAGGGAAAGTTGAAAAGAACTTTGAAGAGAGAGTTCAAGAGGGCGTGAAA
        86
        81147489
        2.0737%
        ACGGCCCTGGCGGAGCGCTGAGAAGACGGTCGAACTTGACTATCT
        86
        76236172
        1.9482%
        ACCACCCTGAACGCGCCCGATCTCGT
        86
        38262809
        0.9778%
        ACGAGATCGGGCGCGTTCAGGGTGGT
        86
        38639073
        0.9874%
        ACCTCTTAACGGTTTCACGCCCTCTTGAACTCTCTCTTCAAAGTTCTTTT
        86
        76176140
        1.9466%
        AGATAGTCAAGTTCGACCGTCTTCTCAGCGCTCCGCCAGGGCCGT
        86
        75473437
        1.9287%
        AGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTA
        86
        108058366
        2.7614%
        GTCGCCGCCGACCCCGTGCGCTCGCTCCGCCGTCCCCCTCTTCGGGGGAC
        86
        45096521
        1.1524%
        GGGGCCACGCGCGCGTCCCCCGAAGAGGGGGACGGCGGAGCGAGCGCACG
        85
        42789848
        1.0935%
        AGAAAAGGTGTTGGTTGATATAGACAGCAGGACGGTGGCCATGGAAGTCG
        85
        16507904
        0.4218%
        GCGGGCCGCCGGTGAAATACCACTACTCTGATCGTTTTTTCACTGACCCG
        85
        16692541
        0.4266%
        GGGCCGCCGGTGAAATACCACTACTCTGATCGTTTTTTCACTGACCCGGT
        85
        26756702
        0.6837%
        CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC
        85
        21350124
        0.5456%
        GCGGACGCTACGCCGCGACGAGTAGGAGGGCCGCTGCGGTGAGCCTTGAA
        85
        23330822
        0.5962%
        ACGGCCCTGGCGGAGCGCTGAGAAGACGGTCGAACTTGACTATCTAGAGG
        85
        16291993
        0.4163%
        CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAT
        85
        13889332
        0.3549%
        AACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCC
        85
        18810722
        0.4807%
        AATGTAGGTAAGGGAAGTCGGCAAGCCGGATCCGTAACTTCGGGATAAGG
        85
        18055346
        0.4614%
        AAATGGGTAAGAAGCCCGGCTCGCTGGCGTGGAGCCGGGCGTGGAATGCG
        85
        12411319
        0.3172%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1